dke-questions > bruker DKI data processing
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Dec 7, 2016 09:12 AM | Ming-Liang Wang
bruker DKI data processing
I am a newer of bruker data postprocesing. Recently, I scaned a few
rats in bruker 7.0T scanner. I wonder if I can process the bruker
DKI data in the GUI. Actually, I got the DCM format DKI data
exported from the scanner. I converted the DCM data to Nifti data
and try to process the DKI data in the GUI. But the DCM data order
seems to be different from the required order of DKE. Besides, we
could not get the gradient bvctor file. If bruker data could not be
processed in the GUI, how could I process the bruker data in
command window. For example, what is the file format exported
from the bruker scanner? How to deal with the order of the images?
I am not fammilar with the command. So, if anyone could tell me the
detailed process. Thans a lot!
Dec 7, 2016 02:12 PM | Emilie McKinnon - MUSC
RE: bruker DKI data processing
Hello Ming-Liang,
It is possible to run DKE with Bruker images. You will have to use the command window. Everything is explained in detail in our manual: http://www.nitrc.org/docman/view.php/652/1918/User%20Manual%202.6.pdf
You can also find some information in our frequently asked questions section:
http://academicdepartments.musc.edu/cbi/...
Let me know if you still run into problems.
Thanks,
Emilie
It is possible to run DKE with Bruker images. You will have to use the command window. Everything is explained in detail in our manual: http://www.nitrc.org/docman/view.php/652/1918/User%20Manual%202.6.pdf
You can also find some information in our frequently asked questions section:
http://academicdepartments.musc.edu/cbi/...
Let me know if you still run into problems.
Thanks,
Emilie
Dec 16, 2016 07:12 AM | Ming-Liang Wang
RE: bruker DKI data processing
Dear Emilie,
Sorry to trouble you again. I have come up with some new problems. As I finally could run DKE in command window with Dcotor Nie in MUSC, it could not run successfully. It sent an error text as follows.
Start date and time: December 16, 2016 13:56:51
Diffusional Kurtosis Estimator (DKE) version 2.6.0
Converting input Bruker images to NIfTI... { Error using textread (line 167)
File not found.
Error in dke_preprocess_bruker>brukeracq (line 303)
Error in dke_preprocess_bruker>bruker2nii (line 212)
Error in dke_preprocess_bruker (line 64)
Error in dke (line 176)
}
MATLAB:textread:FileNotFound
Enclosed are the DKE parameter file. Could you spare some time to read these files to help me find the problem?
Thank you very much! Looking forward to your reply as soon as possible.
Best regards
Ming-Liang Wang
Sorry to trouble you again. I have come up with some new problems. As I finally could run DKE in command window with Dcotor Nie in MUSC, it could not run successfully. It sent an error text as follows.
Start date and time: December 16, 2016 13:56:51
Diffusional Kurtosis Estimator (DKE) version 2.6.0
Converting input Bruker images to NIfTI... { Error using textread (line 167)
File not found.
Error in dke_preprocess_bruker>brukeracq (line 303)
Error in dke_preprocess_bruker>bruker2nii (line 212)
Error in dke_preprocess_bruker (line 64)
Error in dke (line 176)
}
MATLAB:textread:FileNotFound
Enclosed are the DKE parameter file. Could you spare some time to read these files to help me find the problem?
Thank you very much! Looking forward to your reply as soon as possible.
Best regards
Ming-Liang Wang
Dec 16, 2016 03:12 PM | Emilie McKinnon - MUSC
RE: bruker DKI data processing
Hi Ming-Liang,
The problem is that Matlab can not locate your images because the path is incorrect or incomplete.
Try adding a slash after studydir = 'C:\Users\wangmingliang\Desktop\DKEprocessing\';
Also make sure your 2dseq and methods file are located in this folder DKEprocessing.
Hope this helps,
Emilie
The problem is that Matlab can not locate your images because the path is incorrect or incomplete.
Try adding a slash after studydir = 'C:\Users\wangmingliang\Desktop\DKEprocessing\';
Also make sure your 2dseq and methods file are located in this folder DKEprocessing.
Hope this helps,
Emilie
Dec 17, 2016 03:12 AM | Ming-Liang Wang
RE: bruker DKI data processing
Dear Emilie,
Thank you for your timely reply. You are right about the problem. After I complement the full studydir to ".../pdata/1", it began to run. After runing about 35 minutes, however, the DKE end up with a new error. The dke log erroe file is as follows:
{Error using nifti/create>create_each (line 29)
Unable to write header for
"C:\Users\wangmingliang\Desktop\DKEprocessing\DKIdata\pdata\1\intermediate_processing\dki_avg2_nii\adki_500.nii".
Error in nifti/create (line 15)
Error in spm_create_vol>create_vol (line 162)
Error in spm_create_vol (line 16)
Error in spm_write_vol (line 82)
Error in dke_preprocess_bruker>image_avg (line 294)
Error in dke_preprocess_bruker (line 109)
Error in dke (line 176)
}
I wonder if you could tell me the error of my DKI data processing. I am really grateful for all your kind help.
Best regards
Ming-Liang Wang
Thank you for your timely reply. You are right about the problem. After I complement the full studydir to ".../pdata/1", it began to run. After runing about 35 minutes, however, the DKE end up with a new error. The dke log erroe file is as follows:
{Error using nifti/create>create_each (line 29)
Unable to write header for
"C:\Users\wangmingliang\Desktop\DKEprocessing\DKIdata\pdata\1\intermediate_processing\dki_avg2_nii\adki_500.nii".
Error in nifti/create (line 15)
Error in spm_create_vol>create_vol (line 162)
Error in spm_create_vol (line 16)
Error in spm_write_vol (line 82)
Error in dke_preprocess_bruker>image_avg (line 294)
Error in dke_preprocess_bruker (line 109)
Error in dke (line 176)
}
I wonder if you could tell me the error of my DKI data processing. I am really grateful for all your kind help.
Best regards
Ming-Liang Wang